Alex Philippidis Senior News Editor Genetic Engineering & Biotechnology News
10 Countries Meet the Mark for National Genome Projects
As the U.S. marked the 242nd anniversary of its independence, the mother country also had reason to celebrate. England’s National Health Service commemorated its 70th birthday not with a cake or candles, but with a nicely timed announcement that the 70,000th genome had been sequenced of the 100,000 planned by Genomics England, its partner in advancing genomic medicine.
Genomics England is joining the NHS in launching the Genomic Medicine Service, which, beginning October 1, will incorporate genome sequencing into routine medical care. Genomics England was formed in 2013 by the U.K. Department of Health to run the 100,000 Genomes Project, an effort to collect, store, and analyze data from the genomes of patients with rare diseases, their families, and patients with cancer.
The round number of 100,000 genomes has also been the goal of several other nations interested in improving their healthcare—and lowering costs—by carrying out precision medicine based on insights from sequencing data.
Below is a list of initiatives launched by 10 nations toward gathering, storing, and applying genomic data from at least 100,000 genomes, based on information disclosed by the countries, and/or the organizations charged with overseeing the efforts. Included with each listing is a summary of the project, its funding, and recent developments.
Untied Kingdom: 100,000 Genomes Project
Genomics England, the U.K. Department of Health entity created to run the 100,000 Genomes Project, delivered an upbeat progress report in July, disclosing it had sequenced 71,095 whole genomes, and was “well on track” to reach its goal of 100,000 genomes by year’s end.
The project takes its name from the 100,000 whole genomes it has committed to sequencing from around 70,000 National Health Services (NHS) patients; the update coincided with the NHS’ 70th anniversary. According to Genomics England, the Project “has provided the evidence NHS England needs to embed genome sequencing in routine care” through the Genomic Medicine Service (GMS) set to launch in October 2018. Laying a foundation for GMS was among the goals of the project, as were enabling new scientific and medical discoveries, and kick starting the development of a U.K. genomics industry.
The Project uses Illumina services for whole genome sequencing secured through £78 million ($102.4 million) that Genomics England agreed to pay in 2014. Illumina agreed to contribute about £162 million ($212.7 million) toward tools and technologies, and has separately partnered with Genomics England to develop and deliver systems for clinical interpretation, decision support, and knowledge curation. Other funding includes £27 million ($35.5 million) from The Wellcome Trust toward the sequencing hub at its Genome Campus near Cambridge, U.K.; £24 million ($31.5 million) from the U.K. Medical Research Council for computing infrastructure; and up to £20 million ($26.3 million) from the NHS.
Japan: Initiative on Rare and Undiagnosed Diseases
Since 1972, Japan has defined some rare diseases using the phrase “Nan-Byo,” a combination of the words “difficult” and “illness.” However, the classification does not apply to medically unidentified conditions—a challenge the Japan Agency for Medical Research and Development (AMRD) is seeking to address through its Initiative on Rare and Undiagnosed Diseases (IRUD).
Launched in 2015, IRUD is a nationwide medical research consortium that grew to more than 2,000 undiagnosed registrants by December 2016, according to a study published last year in the European Journal of Human Genetics. The consortium is designed to enable primary healthcare clinics to collaborate with more than 400 hospitals including 34 IRUD Clinical Centers, where complex cases can be reviewed by multi-disciplinary IRUD Diagnosis Committees of medical specialists and clinical geneticists. In addition to the clinical centers and committees—which are supported by about 500 physicians and 50 coordinators—IRUD includes four analysis centers and a data center.
IRUD has been funded annually at between ¥600 million to ¥700 million ($5.4 million to $6.3 million).
“We acknowledge that the majority of registered patients remain undiagnosed even after mutual referral within the cluster of related research consortia,” a team of AMRD researchers stated in the study. “However, intensive research on specific cases, accompanied by training for nationwide collaborators by the IRUD network, will potentially lead to diagnostic and therapeutic innovations in both the short- and long-term.”
AMRD has laid out three “next steps” or future initiatives to build on IRUD research. The initiatives, dubbed “IRUD Beyond,” include developing innovative drug candidates by targeting novel, single pathological mutations discovered through the Initiative, applying new technologies to cases that remain unsolved after NGS-based genome analysis, and facilitating international data sharing.
One key effort, AMRD said, by which IRUD plans to seek further data-sharing opportunities and ensure patients are given the best chance of receiving a diagnosis, is through participation in international efforts, notably the International Rare Diseases Research Consortium (IRDiRC).
China: 100,000 Genomes Project
China’s 100,000 Genomes Project launched in December 2017 as the nation’s first major national human genome research effort. It is one of numerous initiatives through which China intends to fulfill a component of its 13th Five–Year Plan (2016–2020) identified genomics as an area worthy of direct investment.
The Project is led by researchers at Harbin Institute of Technology (HIT) who will sequence the genomes of 100,000 people from different ethnic backgrounds and regions across China, from the Han ethnic majority to nine minorities with a combined population of 5 million, including the Zhuang and Hui peoples.
“Its main goal is to study how Chinese people transform from health to disease, environmental impacts, and the interactions between environmental factors and genes, and its influence on people’s health,” Prof. Wang Yadong, chief scientist of the 100,000 Genomes Project and principal scientist and president of HIT’s School of Computer Sciences and Technology and the Institute of Biological Information Technology, told China Global Television Network.
The Project will consist of three phases. The first is a demonstration project to sequence the genomes of 10,000 people. The second will compile sequencing and phenotype data from 50,000 people and will use the data to draw genome and health maps for all 60,000 people sequenced at that point. In the third phase, researchers will complete the genome and health maps of all 100,000 genomes. The Project is in its initial gene sample collection stage, Yu Jun, Ph.D., former deputy head of the Beijing Institute of Genomics under the Chinese Academy of Sciences (CAS), told Global Times, an English-language newspaper published by People’s Daily, the official newspaper of the Chinese Communist Party.
Yu said the Project will include a “health contrast” pool of genetic data from people with various diseases in order to study correlations between specific genes and specific diseases, such as diabetes. The program is projected to take four years, and is funded by China’s Ministry of Science and Technology, with HIT stating the initiative will cost an estimated RMB 89.85 million
Australia: Australian Genomics Health Futures Mission
One of the newest public genome research initiatives launched in May in Australia, is The Australian Genomics Health Futures Mission. It was launched after the national government led by Prime Minister Malcolm Turnbull committed A$500 million (about $370 million) over the next 10 years for the nation’s first national human genome project.
The Mission is intended to foster and fund new research, clinical trials, and technologies, all with the goal of helping Australians to live longer and better by expanding access to genomics knowledge and technology. The Mission’s first project, at A$20 million (nearly $15 million), is “Mackenzie’s Mission,” a pre-pregnancy screening program designed to detect rare and debilitating genetic birth disorders. The project is named for Mackenzie Casella, who last year lost her life to spinal muscular atrophy (SMA).
Components of the Mission include new and expanded “flagship” clinical studies of rare diseases, rare cancers, and complex conditions; clinical trials designed to help translate technology applications into patient care; and increased academic and research collaborations. The initiative will also develop national standards and protocols to enhance data gathering and analysis; facilitate dialogue promote the value of genomics to the broader community; and encourage government partnerships with philanthropists and businesses.
One such partnership was announced in June, when the government agreed to provide A$2 million (about $1.5 million) to the Cerebral Palsy Alliance Research Foundation. The funding is intended to support four research priorities: making early diagnosis and treatment of cerebral palsy the standard of care in Australia, clinical trials of new interventions in high risk infants, a trial of TheraSuit intensive therapy, and new therapies during pregnancy designed to prevent cerebral palsy.
“It is my hope that further research and advancement in medical technology including genomics will change the lives of those with cerebral palsy. Many cases of cerebral palsy have been shown to have a genomics link,” stated Australia’s Health Minister Greg Hunt.
Saudi Arabia: Saudi Human Genome Program
The Saudi Human Genome Program aims to sequence 100,000 samples (normal and disease) from the Saudi population over five years.
Saudi Arabia’s population of roughly 32 million may seem low to Westerners, yet Saudi Arabia is concerned about its high rate of severe inherited diseases. These impact 8% of births in the Kingdom, as well as its higher rate of common genetic disorders; more than 20% of the population has diabetes, and more than 30% is affected by obesity. Another health challenge is the Kingdom’s 57% consanguinity rate, mostly through first-cousin marriages. Authorities blame the high prevalence of genetic disease for the $30 billion-plus spent annually by Saudi Arabia on healthcare.
The Saudi Arabian government has approved $200 million over five years for the King Abdulaziz City for Science and Technology (KACST)—the agency charged with supporting scientific research—toward the Program. KACST joined Life Technologies (since acquired by Thermo Fisher Scientific) in launching the program in 2013. Soon after, the price of oil fell globally, leading to reported delays in funding the project.
Yet progress has been made. As of the end of 2016, according to KACST, the Saudi Human Genome Program has developed 13 gene panels covering more than 5,000 inherited diseases, and sequenced more than 10,000 samples from Saudi patients with inherited diseases that resulted in identification of more than 2,000 variants underlying the diseases—including more than 500 “Saudi mutations” represented in multiple patients. Saudi-specific mutations alone cost the Kingdom SR 6.4 billion ($1.7 billion) annually.
United States: All of Us Research Program
Gleaning health and wellness data from 1 million or more Americans is the goal of the NIH’s All of Us Research Program, which opened for national enrollment on May 6. People ages 18 and older are eligible to enroll, regardless of health status. Those who enroll join more than 25,000 participants who signed up for All of Us during a beta phase.
In addition to enrolling 1 million-plus participants, All of Us aims to become the nation’s largest and most diverse research cohort, with plans to oversample communities underrepresented in past research. Eric Dishman, a kidney cancer survivor who directs All of Us, told the website FiveThirtyEight the program aims to have 70% to 75% of its data contributed by underrepresented people, including women and people of color.
To generate genotype and whole genome sequence data, the NIH plans to fund up to two genome centers in the current federal fiscal year, which ends September 30. Each center is expected to spend up to $15 million in the first year, when both centers are to generate and analyze data from 100,000 participants. That number rises to 200,000 participants annually in years 2 through 5.
All of Us participants will also share health and lifestyle information, collected from online surveys and data from electronic health records (EHRs). The surveys are designed to learn more about participants’ overall health and habits and where they live and work. The EHR data will information related to medical histories, treatment effectiveness, and side effects.
All of Us is a component of the Precision Medicine Initiative (PMI), launched in the 2016 fiscal year when $130 million was allocated to NIH to build a national cohort, and $70 million was allocated to the NIH’s National Cancer Institute to lead efforts in cancer genomics as part of PMI for Oncology. The NIH has drawn upon more than 100 organizations to carry out the
Estonia: Personalized Medicine Programme
Estonia launched its Personalized Medicine Programme in 2016, and began its most recent initiative in April, when it marked its official effort to recruit and genotype an additional 100,000 participants for the Estonian Biobank. Estonians are invited to participate in genome-wide genotyping that will be translated into personalized reports for use in everyday medical practice through the national e-health portal.
The program was initiated “in order to boost the development of personalized medicine in Estonia and thus contribute to the advancement of preventive healthcare,” Jevgeni Ossinovski, Minister of Health and Labour, said in a statement.
Estonia’s government has allocated €5 million ($5.8 million) this year for the initiative, which is a joint project of Estonia’s Ministry of Social Affairs, the National Institute for Health Development, and the Estonian Genome Center of the University of Tartu. The National Institute is coordinating the project while the genome center has maintained and studied the DNA of the nation’s first biobank participants, numbering more than 50,000.
That initial cohort of 51,535 gene donors (≥18 years of age) closely reflects the age, sex, and geographical distribution of the Estonian population, according to the genome center. Among the program participants Estonians represent 83%, Russians 14%, and other nationalities 3%.
Information from the Biobank is being linked with national registries and hospital databases in order to obtain updated phenotypic information, including endpoints and nonfatal events.
France: France Génomique (Médicine France Génomique 2025 or French Plan for Genomic Medicine 2025)
France launched its public genomics initiative in 2016, saying it would invest €670 million ($782 million) over the first five years, including €230 million ($268.5 million) from the corporate sector, toward a network that will encompass 12 genomic sequencing centers or “platforms” and two centers specializing in genomic know-how and data analysis.
France Génomique’s progress to date includes eight sequencing platforms that have emerged, as have another 12 platforms specializing in bioinformatics. A Big Data computing center, the TGCC (Très Grand Centre de Calcul), was established at the CEA (French Commission for Atomic Energy and Alternative Energies). Within TGCG is the Computer Centre for Research and Technology, which has configured an extension dedicated to the needs of France Génomique users.
France Génomique intends to grow France into a leader in genomic medicine, integrate genomic medicine into routine patient care, and establish a genomic medicine industry to fuel economic growth. By 2020, France aims to have increased its annual sequencing capacity to 235,000 genomes—of which 175,000 are to come from cancer patients, and the remaining 60,000 from rare disease patients. Cancer, rare diseases, and diabetes are the initiative’s initial disease areas of focus, with other common diseases added to the mix by 2020.
“Genomic medicine is a revolution in the area of care and prevention,” declared Yves Levy, chairman and CEO of Inserm and chairman of the National Alliance for Life Sciences and Health (Aviesan), a stakeholder coalition of science and biomedical research centers that oversees the French Plan for Genomic Medicine 2025. “France must find a way to achieve this revolution, and take its place among the leaders.”
Earlier this year, Inserm and Aviesan joined Genomics England, which oversees the U.K.’s 100,000 Genomes Project, in articulating a joint vision for the countries of becoming nothing less than the most advanced and competitive genomics research and healthcare systems in the world.
Dubai, United Arab Emirates: Dubai Genomics
Dubai’s slogan is “Always being 10 years ahead of other world cities.” With that in mind, the Dubai Health Authority launched Dubai Genomics earlier this year, a human genome initiative that intends to sequence all of its 3 million residents. Dubai Genomics is one of numerous projects within the Dubai Future Foundation’s “Dubai 10X Initiative,” launched to catapult the emirate 10 years ahead of the rest of the world in all sectors by implementing disruptive technologies first.
The project’s first phase will take at least 24 months and focus on building a genomic medicine infrastructure and starting large-scale whole-genome sequencing. That work, said Dubai Genomics, will include collecting samples from UAE nationals, analyzing DNA sequencing data, and recording results. The second phase will deploy artificial intelligence capabilities for more complex sequence analysis layered with longitudinal data, using what the authority terms a ”massive” genomic databank. The goal is to accurately predict risks associated with genetic-related illnesses.
The third phase, Dubai intends to collaborate with pharmaceutical companies and academia to develop new precision medicine treatments. The Authority has directed several affiliate organizations to carry out the initiative, including the department of pathology and genetics, and the Dubai Cord Blood and Research Center (DCRC).
“Forming genome laboratories in Dubai signals a new phase, where our forecasts for the future of the health and medical services sector begin to materialize,” Humaid Mohammed Al Qatami, DHA’s director general and chairman of the board, told Dubai’s Khaleej Times. “The labs will establish the first national genetic database for future research, lending support to decision-makers as they set plans and strategies for the future of the healthcare sector. This, in turn, ensures Dubai’s global competitiveness and strengthens the knowledge economy.”
Turkey: Turkish Genome Project
Turkey’s Ministry of Health in February launched the Turkish Genome Project, which aims to sequence the genomes of 100,000 Turks over three years in the first phase. The second phase is far more ambitious, with plans to increase that number to 1 million genomes sequenced by 2023, the 100th anniversary of the present-day Republic of Turkey. The project aims to create a national DNA map that will offer researchers clues to fighting disease.
“The Turkish Genome Project has two goals: mapping out our genetic structure and finding out reasons behind prevalence of chronic diseases such as cancer, or reasons behind longevity in a certain population group,” Prof. Fahrettin Kelestemur, president of Turkey’s recently founded Directorate of Health Institutes (TÜSEB), which oversees the Project, told the country’s Anadolu news agency.
One component of the project will focus on complex phenotypes with high rates of heritability, such as obesity, diabetes, cardiovascular disease, neuropsychiatric conditions, endocrine function, and rheumatologic diseases, while other components will focus on rare diseases, and cancer, Tayfun Özçelik, M.D., of Bilkent University, whose research focuses on neurodevelopmental disorders, wrote in the journal Molecular Genetics and Genomic Medicine.
This article was originally published in the September/October 2018 issue of Clinical OMICs. For more content like this and details on how to get a free subscription, go to www.clinicalomics.com.